This invention relates to cryptology, which is the science of encrypting and decrypting messages, to steganography, which is the concealment of the presence of secret messages, and also to nucleic acid chemistry and molecular biology. In particular, the invention relates to (a) encrypting information in the form of words, numeric data, or graphical images, by obtaining a set of nucleic acid strands or nucleic acid analog strands having subunit sequences selected to represent the information, so that the information cannot be decrypted by anyone not in possession of a key for decryption, (b) transmitting the set of nucleic acid strands or nucleic acid analog strands to a recipient who possesses a key for decryption, and (c) decrypting the information by using the key to recover the words, numeric data, or graphical images, represented by the nucleic acid strands or nucleic acid analog strands.
All publications, patents, and patent applications cited herein are incorporated by reference, fully as if each individual publication, patent, or patent application was specifically and individually indicated to be incorporated by reference.
Over the centuries, many different methods have been developed to send messages or other information in a form that cannot be understood by anyone other than the intended recipient. Such methods have typically involved encrypting the information by replacing the letters or numbers, words, or phrases of the message with other letters and/or numbers. Decryption of the information is achieved through use of a key which may include instructions and other information, special materials, and a device, and which enables the recipient to recover the original message or information from the encrypted communication (Fred B. Wrixon, Codes and Ciphers, Prentice Hall, New York, N.Y., 1992).
Today, computers and other electronic devices are used to encrypt, transmit, and decrypt private communications. For example, an optical scanner can be used to digitize a graphical image. The two-dimensional matrix of digital values that defines the image can be encrypted, electrical signals representing the encrypted image can be transmitted over a communications link, and the recipient can use a decryption key to recover the digitized image (see Virga, U.S. Pat. No. 5,398,283; and Luther, U.S. Pat. No. 5,533,127).
Oligonucleotides and oligonucleotide analogs of defined sequence and length are currently used in many different molecular biological, biochemical, diagnostic, and computational applications. For example, they are used as hybridization probes to detect specific nucleic acid sequences in DNA and RNA samples immobilized on a variety of filter and solid supports, as in DNA and RNA Dot, Southern, and Northern blots, and in colony and plaque hybridization assays. These methodologies are widely used in the isolation and cloning of specific nucleic acids, and the diagnosis of disease caused by pathogens and genetic mutations (Berent et al., BioTechniques, issue of May/June 1985, pages 208-20; and J. Sambrook, E. F. Fritsch, and T. Maniatis, Molecular Cloning, A Laboratory Manual, Cold Spring Harbor Laboratory Press, Cold Spring Harbor, N.Y., 1989, Chapter 11).
Sets of oligonucleotides of defined sequence are also used as primers for polymerases in polynucleotide synthesis and in nucleic acid amplification, for example, by the polymerase chain reaction (PCR, Erlich, PCR Technology, Principles and Applications for DNA Amplification, Stockton Press, New York, N.Y., 1989, in entirety), or by strand displacement amplification (SDA, Fraiser et al., U.S. Pat. No. 5,648,211, col. 3-18).
Oligonucleotides of defined sequence are also used as probes of macromolecular structure and function; for example, antisense and triplex-forming oligonucleotides can be screened to identify oligomers which bind specifically to an accessible portion of a native target nucleic acid such as a folded mRNA molecule, and which inhibit transcription or translation of a specific mRNA (see, for example, Milner et al., Nature Biotechnology, 1987, Vol. 15, pages 537-41; and Hogan et al., U.S. Pat. No. 5,176,996, in entirety).
Various strategies for finding solutions to mathematical problems have been devised which use sets of oligonucleotides having selected length and sequence properties to represent elements of the problems. DNA oligonucleotides representing vertices or edges of a graph have been used to solve a Hamiltonian path problem (Adleman, Science, 1994, Vol. 266, pages 1021-3) and a xe2x80x9csatisfactionxe2x80x9d problem (Lipton, Science, 1995, Vol. 268, pages 542-5); oligonucleotides representing non-negative binary numbers have been used for performing addition (Guarnieri et al., Science, 1996, Vol. 273, pages 220-223); and oligonucleotides representing products of matrix elements have been used for performing matrix multiplication (Oliver, J. Molecular Evolution, 1997, Vol. 45, pages 161-7).
Recently, oligonucleotides have been immobilized or synthesized in micro-arrays on solid supports of material such as glass or SiO2. xe2x80x9cDNA chipsxe2x80x9d produced in this manner are useful for detecting or capturing multiple nucleic acid targets, for determining the nucleic type sequence of a target nucleic acid, for simultaneous analysis of the expression of thousands of genes, large scale gene discovery, DNA polymorphism screening, and mapping of genomic DNA clones, and are well suited for use in medical diagnostic assays for detection of pathogen infection and genetic mutation (for example, see Fodor et al., U.S. Pat. No. 5,445,934, col. 3-21, 23-32; McGall et al., U.S. Pat. No. 5,412,087, col. 4-20; Cantor, U.S. Pat. No. 5,503,980, col. 4-20; Heller et al., U.S. Pat. No. 5,605,662, col. 9-32; McGall et al., J. American Chem. Soc., 1997, vol. 119, pages 5081-90; A. C. Pease et al., 1994, Proceedings of the National Academy of Sciences, Vol. 91, pages 5022-6; and reviews by Ramsay, Nature Biotechnology, 1998, Vol. 16, pages 40-44; and Marshall et al., Nature Biotechnology, 1998, Vol. 16, pages 27-31). Nucleic acid hybridization arrays such as those on DNA chips permit quick and accurate detection of soluble oligonucleotides in a sample having a specific nucleotide sequence.
A nucleic acid hybridization array can also be used as an oligonucleotide storage device from which oligomers having selected nucleotide sequences can be obtained, as described in U.S. application Ser. No. 09/078,761 filed May 15, 1998. To accomplish this, single-stranded oligomers tethered to a hybridization array are hybridized to saturation with complementary oligonucleotides. Soluble oligonucleotides having a desired sequence can then be selectively released from individual array sites by localized denaturation, e.g., by localized heating of the array sites at which the desired oligonucleotides are hybridized.
Oligonucleotides and their analogs are now shown to be particularly suitable for representing information such as letters, words, or phrases of a body of text, numeric data, or the digital values that define a graphical image. Among the properties of oligonucleotides which favor their use in this manner are their ability to store large amounts of information as ordered sequences of nucleotides, their ability to be amplified, the rapid recognition and high-affinity hybridization of complementary strands, the availability of a large number of different enzymes and procedures for chemically modifying nucleic acid oligomers, and the ability to quickly and efficiently obtain and detect oligonucleotides having selected nucleotide sequences, using methods employing nucleic acid hybridization arrays or chemical synthetic and sequencing procedures.
The invention provides methods for encrypting information, such as letters, words or numeric data of a message, or digital values that define a graphical image, by obtaining a set of nucleic acid strands or their analogs having selected nucleotide sequences that represent the information. Decryption of the information is accomplished by using a key that identifies the information represented by the nucleotide sequences of the nucleic acid strands. Preferably, the nucleic acid strands or nucleic acid analog strands that are used to represent encrypted information are oligonucleotides or oligonucleotide analogs. Nucleic acids have very high information storage density; a set of 100 copies of each of 1010 different 40-mer oligonucleotide sequences, each representing a different letter, word, phrase, or set of digital values, has a mass that is significantly less than a microgram. Thus, information that is encrypted as a set of oligonucleotides can be transmitted to an intended recipient in a form that is nearly undetectable, and can only be understood by someone in possession of a key for decryption.
The invention provides methods comprising obtaining oligonucleotides or their analogs having selected nucleotide sequences representing encrypted information by releasing them from an oligomer-storing device comprising a nucleic acid hybridization array.
The invention also provides methods comprising detecting nucleic acids or their analogs having selected nucleotide sequences representing encrypted information by allowing them to hybridize specifically to a nucleic acid hybridization array, and by detecting the array sites at which they are hybridized.
The invention further provides methods giving multiple additional levels of decryption, comprising:
(i) scrambling the order of the sites in a nucleic acid hybridization array that is used to detect oligomers representing the encrypted information, relative to the order of the sites in the depot array from which the oligomers representing the encrypted information are obtained;
(ii) providing one or more sets of bridging oligomers that specifically hybridize to the oligomers attached to the array sites of a nucleic acid hybridization array, and/or to the oligomers representing the encrypted information, and/or to other bridging oligomers, so as to permit attachment of the oligomers representing the encrypted information to the corresponding sites of said nucleic acid hybridization array; and
(iii) providing a set of detectable signal oligomers that specifically hybridize to the oligomers representing the encrypted information, or to bridging oligomers that specifically hybridize thereto, so as to permit detection of the oligomers representing the encrypted information.
The invention also provides methods for transmitting the nucleic acid strands representing the encrypted information to the intended recipient as a solute dissolved in an aqueous solvent, as dried solid matter sealed in a container or adhering to a surface of a co-transmitted article, or as a portion of a larger single- or double-stranded synthetic polynucleotide or recombinant plasmid, plastid, viral, or cellular nucleic acid.
The invention further provides a method for tagging an article with information which identifies the article, wherein xe2x80x9ctagsxe2x80x9d comprising nucleic acids or their analogs having selected nucleotide sequences are reversibly attached to the article. The article so tagged can be identified by removing some of the nucleic acid and identifying their nucleotide sequences.